VolSurf manual

Table of Contents

I. The VolSurf package

1. Overview

1.1. What is Volsurf?
1.2. VolSurf descriptors and features
1.3. What VolSurf is not?
1.4. Program citation.
1.5. Program organization
1.6. Limitations.
1.7. User's support.

2. Changes from previous editions

2.1. New VolSurf descriptors
2.2. New library models
2.3. Improved library models
2.4. New way to handle library models
2.5. Faster MIFs calculation
2.6. Automatic Protonation-Deprotonation
2.7. Handling of binary Vol files
2.8. New method for charge distribution calculation
2.9. Confidence interval
2.10. Easier handling of large series of compounds
2.11. More user settings
2.12. User manual in pdf format

3. Installation

3.1. Obtaining and installing licenses
3.2. Shared libraries requirements
3.3. Customising VolSurf look

4. Background

4.1. 3D maps
4.2. From 3D maps to 2D descriptors
4.3. Multivariate analysis of VolSurf descriptors
4.4. References

5. Overview of the programme GRID

5.1. Energy functions of programme GRID
5.2. VolSurf Probes

6. VolSurf Descriptors

6.1. Meaning of VolSurf descriptors

7. Statistical Tools

7.1. Principal Components Analysis (PCA)
7.2. Partial Least Squares (PLS)
7.3. Variable selection

8. Volsurf Library models

8.1. Blood-Brain Barrier permeation model (BBB)
8.2. Termodinamic solubility model (SOLY)
8.3. Caco2 permeation model (CACO2)
8.4. Biopharmaceutical classification model (SolyPerm)
8.5. Protein Binding model (Protein_Binding)
8.6. Volume of Distribution model (Volume_Distribution)
8.7. hERG model (HERG)
8.8. Water / DMSO solubility model (solDMSO)
8.9. CYP3A4 Metabolic Stability model (MetabolicStability)

9. Command line options

9.1. Command file syntax
9.2. Command file examples
9.3. Commands description

II. VolSurf reference

10. Menu File (Alt-F)

10.1. File->Open data file... (Alt-O)
10.2. File->Import
10.3. File->Expand series...
10.4. File->Export data file
10.5. File->Object type
10.6. File->Model library...
10.7. File->Direct prediction...
10.8. File->Data file utils...
10.9. File->Quit (Alt-Q)

11. Menu Calculation (Alt-C)

11.1. Calculation->Recompute...

12. Menu Pretreatment (Alt-R)

12.1. Pretreatment->Scale...
12.2. Pretreatment->F. Factorial selection...
12.3. Pretreatment->Exclude vars.
12.4. Pretreatment->Exclude objects
12.5. Pretreatment->Reload original

13. Menu List (Alt-L)

13.1. List->Method info
13.2. List of X matrix descriptors
13.3. List->Activity
13.4. List->PCA scores

14. Menu Modeling (Alt-M)

14.1. Modeling->Generate PCA model...
14.2. Modeling->Generate PLS model...
14.3. Modeling->Validate PLS model...
14.4. Modeling->External PCA pred...
14.5. Modeling->External PLS pred...
14.6. Modeling->Project on library model
14.7. Modeling->Select subset...

15. Menu Plot (Alt-P)

15.1. Plot->Descriptors
15.2. Plot->2D plot
15.3. Plot->3D plot
15.4. Plot->Grid plot
15.5. Plot->Profile

16. Menu Preferences (Alt-S)

16.1. Preferences->Directories
16.2. Preferences->Files
16.3. Plot configuration
16.4. Preferences->Miscellaneus
16.5. Preferences->Grid Plot

17. Menu Help (Alt-H)

17.1. Help->About...
17.2. Help->Help browser

III. External applications

18. 2D plot application

19. 3D plot application

20. dgram application

21. plotGrid application

21.1. Drag and drop import
21.2. Mouse and plotGrid modes
21.3. plotGrid menu

22. profile application

IV. VolSurf tutorials

23. Tutorial 1

23.1. VolSurf in a set of passively absorbed drugs

24. Tutorial 2

24.1. VolSurf in Combinatorial Chemistry

25. Tutorial 3

25.1. HSA protein binding
25.2. Biopharmaceutical classification

Colophon

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